msImpute

DOI:10.18129/B9.bioc.msImpute

This is thedevelopmentversion of msImpute; for the stable release version, seemsImpute.

Imputation of label-free mass spectrometry peptides

Bioconductor version: Development (3.16)

MsImpute is a package for imputation of peptide intensity in proteomics experiments. It additionally contains tools for MAR/MNAR diagnosis and assessment of distortions to the probability distribution of the data post imputation. The missing values are imputed by low-rank approximation of the underlying data matrix if they are MAR (method = "v2"), by Barycenter approach if missingness is MNAR ("v2-mnar"), or by Peptide Identity Propagation (PIP).

Author: Soroor Hediyeh-zadeh [aut, cre]

Maintainer: Soroor Hediyeh-zadeh

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("msImpute")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

查看文档的版本包age installed in your system, start R and enter:

browseVignettes("msImpute")

HTML	R Script	msImpute: proteomics missing values imputation and diagnosis
PDF		Reference Manual
Text		NEWS

Details

biocViews	MassSpectrometry,Proteomics,Software
Version	1.7.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	GPL (>=2)
Depends	R (>= 3.5.0)
Imports	softImpute, methods, stats, graphics,pdist,reticulate,scran,data.table,FNN,matrixStats,limma,mvtnorm,tidyr,dplyr
LinkingTo
Suggests	BiocStyle,knitr,rmarkdown,ComplexHeatmap,imputeLCMD
SystemRequirements	python
Enhances
URL
BugReports	https://github.com/DavisLaboratory/msImpute/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	msImpute_1.7.0.tar.gz
Windows Binary	msImpute_1.7.0.zip
macOS 10.13 (High Sierra)	msImpute_1.7.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/msImpute
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/msImpute
Package Short Url	//www.andersvercelli.com/packages/msImpute/
Package Downloads Report	Download Stats